rs3803808

chr17-2049683-G-Achr17-2049683-G-Cchr17-2049683-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007065576.1(LOC124903896):n.267C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 152,238 control chromosomes in the GnomAD database, including 990 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.060 (990 hom., cov: 32)
• Consequence: LOC124903896 XR_007065576.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

Genes affected

LOC124903896 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903896	XR_007065576.1	n.267C>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0600 AC: 9125 AN: 152122 Hom.: 991 Cov.: 32

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0689

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0367

Gnomad OTH AF: 0.0479

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0600 AC: 9131 AN: 152238 Hom.: 990 Cov.: 32 AF XY: 0.0671 AC XY: 4992 AN XY: 74440

Gnomad4 AFR AF: 0.0117

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0689

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.0805

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0366

Gnomad4 OTH AF: 0.0498

Alfa AF: 0.0455 Hom.: 38

Bravo AF: 0.0580

Asia WGS AF: 0.254 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	8.4
Dann	Benign	0.90

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3803808; hg19: chr17-1952977;